The idea that the microbial communities within the GI tract have a profound influence on general human health actually originated with Russian scientist Elie Metchnikov at the turn of the last century. These writings prompted Japanese scientist Minoru Shirota to begin investigation of how fermentative bacteria improve health. He succeeded in isolating a strain of Lactobacillus that could survive passage through the intestine, while promoting a healthy balance of microbes. The "Shirota strain" is still used today in the fermented beverage Yakult. This book opens with two general reference chapters, which provide an overview of current knowledge of gastrointestinal immunology and the commensal microbiology of the gut. Next are two chapters dedicated to current methodologies used to investigate the microbiota and host: molecular analysis of microbial diversity and gnotobiotic research. Both positive and negative interactions between the microbiota and the immune system can take.